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Computational Approaches to Biochemical Reactivity

  • Book
  • © 2002

Overview

Editors:
  1. Gábor Náray-Szabó

    1. Department of Theoretical Chemistry, Eötvös Loránd University, Budapest, Hungary

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    You can also search for this editor in PubMed   Google Scholar

  2. Arieh Warshel

    1. Department of Chemistry, University of Southern California, Los Angeles, USA

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

Part of the book series: Understanding Chemical Reactivity (UCRE, volume 19)

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Table of contents (9 chapters)

  1. Front Matter

    Pages i-x
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  2. Quantum Mechanical Models for Reactions in Solution

    • J. Tomasi, B. Mennucci, R. Cammi, M. Cossi
    Pages 1-102

  3. Free Energy Perturbation Calculations within Quantum Mechanical Methodologies

    • Robert V. Stanton, Steven L. Dixon, Kenneth M. Merz Jr.
    Pages 103-123

  4. Hybrid Potentials for Molecular Systems in the Condensed Phase

    • Martin J. Field
    Pages 125-151

  5. Molecular Mechanics and Dynamics Simulations of Enzymes

    • Roland H. Stote, Annick Dejaegere, Martin Karplus
    Pages 153-198

  6. Electrostatic Interactions in Proteins

    • Kim A. Sharp
    Pages 199-235

  7. Electrostatic Basis of Enzyme Catalysis

    • G. Náray-Szabó, M. Fuxreiter, A. Warshel
    Pages 237-293

  8. On the Mechanisms of Proteinases

    • A. Goldblum
    Pages 295-340

  9. Modelling of Proton Transfer Reactions in Enzymes

    • Johan Åqvist
    Pages 341-362

  10. Protein-Ligand Interactions

    • Terry P. Lybrand
    Pages 363-374

  11. Back Matter

    Pages 375-380
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Keywords

About this book

A quantitative description of the action of enzymes and other biological systems is both a challenge and a fundamental requirement for further progress in our und- standing of biochemical processes. This can help in practical design of new drugs and in the development of artificial enzymes as well as in fundamental understanding of the factors that control the activity of biological systems. Structural and biochemical st- ies have yielded major insights about the action of biological molecules and the mechanism of enzymatic reactions. However it is not entirely clear how to use this - portant information in a consistent and quantitative analysis of the factors that are - sponsible for rate acceleration in enzyme active sites. The problem is associated with the fact that reaction rates are determined by energetics (i. e. activation energies) and the available experimental methods by themselves cannot provide a correlation - tween structure and energy. Even mutations of specific active site residues, which are extremely useful, cannot tell us about the totality of the interaction between the active site and the substrate. In fact, short of inventing experiments that allow one to measure the forces in enzyme active sites it is hard to see how can one use a direct experimental approach to unambiguously correlate the structure and function of enzymes. In fact, in view of the complexity of biological systems it seems that only computers can handle the task of providing a quantitative structure-function correlation.

Editors and Affiliations

  • Department of Theoretical Chemistry, Eötvös Loránd University, Budapest, Hungary

    Gábor Náray-Szabó

  • Department of Chemistry, University of Southern California, Los Angeles, USA

    Arieh Warshel

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